We studied the relation between cortical oscillatory rhythms and the structural integrity of the corpus callosum in 21 children with spina bifida and hydrocephalus. Participants underwent resting state neuromagnetic recordings and diffusion tensor imaging. Areas of three segments of the corpus callosum (genu, body, splenium) were derived through diffusion tensor imaging-based morphometrics. Children with spina bifida showed reduced values of spectral power in the theta, alpha and beta bands when compared with age-matched controls, but only in the posterior and temporal regions. Reduced spectral power in posterior regions correlated with decreased area of the posterior segments of the corpus callosum. Atypical cortical oscillatory activity is associated with reduced transcallosal connectivity in children with spina bifida.